Python

Events

This material is being used during the online events organized in the Code-Mavens Meetup group.

Chat

How to select a Python project to contribute to?

Pick a Python-based project you use.
Pick a Python module that your code directly depends on. They are listed in requirements.txt or pyproject.toml.
Pick a Python module that your code indirectly depends on. They are listed in constraints.txt, uv.lock.
Search on GitHub: A semi-popular, recently updated Python project stars:100..1000 pushed:>2025-10-01 language:Python
For now I’ll pick some of the scientific libraries. e.g. Biology-related libraries.
Ask ChatGPT to suggest other science-related libraries.
Pick a popular project and work on stale PRs. That is PRs where there is already good work, but the original author (of the PR) has vanished.
PyDigger - once it is fixed.

What and how to contribute to a Python project?

Link to VCS: Does the project listing in Pypi link to its public VCS? If not, try to find the VCS and the first PR could be adding this link. If you can’t find the VCS then the rest will be rather irrelevant. Maybe send an email to the author asking if there is a public VCS?
Testing: Try to run the tests locally or better yet in a Docker conatiner.
- Python testing demo
- Python testing
- Generate test coverage report
CI
- If there are tests, check if there is a CI?
- Setting up CI: GitHub Actions or GitLab pipelines.
- Updating the GitHub actions if necessary.
Dependencies
- Add dependabot for GitHub Actions and for the dependencies.
Code formatting
- Using black check if the code is well formatted. If not open an issue suggestion to do it. black --check .
- See also autopep8.
Linting
- Run one or more linters on the code. Add, linter configuration to the project. Setup CI to run the linter(s).
- Pylint
- Flake8
- ruff
- PyChecker
- Pylama
- Sonar?
- Codacy?
Add type annotation
- Start by running one of the type-checking tools on the code-base. Add configurations to the repository. Setup CI to run the type-checker.
- mypy
- pytype
- Python types
- Python types at PyWeb 2025.05
Fuzz testing
- atheris
Mutation testing
- mutatest
- mutmut
- MutPy
Code complexity analyzis
- code-complexity-analyzer
- complexipy
Refactoring
Code reading
Convert setup.py to pyproject.toml.

Project reports

genomebundle
- 2026.03.09
- It does not have a CI (and its repository is not listed on the pydigger web site)
- It does not have tests
- After some 20 minutes as I see the usage takes a long time, I gave up trying to write a test.
qrcode-pretty
- 2026.02.03
- PR: added test for generated images by nnguyen-cs (Ted) - Merged ✅
- Video recordings 🎦
- PR: Add the GitHub Actions to run the test on every push by nnguyen-cs (Ted) - Merged ✅
- Video recordings 🎦
- TODO: we could add further tests, parametrizing the current one, check if there are flags we can use, add more python versions to the CI.
- TODO: generated test coverage report.
factpages-py
- 2026.01.20
- Issue: Readme has some slightly confusing info - Closed ✅
- PR: Add some tests based on the documentation - Merged ✅
- Learn: build A simple, correct Python build frontend.
- Learn: twine a utility for publishing Python packages on PyPI.
- 2026.01.23
- We used the Docker container to get test coverage:
- pip install pytest-cov
- pytest --cov=factpages_py --cov-report html --cov-branch
- It is 24%
- We tried to call the field_summary method in analysis.py without success.
- Issue: How to call field_summary in analysis.py ? - Implemented ✅
- Add more tests - TODO 🎁
- 2026.03.09
- I the docker container
- virtualenv venv
- source venv/bin/activate
- pip install pytest-cov
- Coverage is 44%
- Issue: Allow ci to run on other branches or manually
- PR: Add dependabot configuration
- PR: add tests exporting data to temporary folder
- TODO: add tests importing data from json and other file format
scikit-learn
- 2026.01.11
- Setting up the development environment is explained well but still takes time.
- Also running the tests took 10 minutes on my computer.
- Maybe create a development environment in a Docker image and share the instructions how to use it.
- Maybe describe how to use uv to setup the development environment.
- Issue: confusion_matrix crashes when sample_weight is an empty array - we tried to reproduce it and commented on it. - Issue closed. ✅
- We opened a few issues on the PyDigger project.
readanybook
- We encountered this project, but we could not find its GitHub repository. Someone mentioned that it might be related to some pirated books.
- I don’t know, but apparently one has to be carefull not to contribute to some illegal activity.
paperpipe
- 2026.01.11
- PR: Add Dependabot configuration for version updates - Merged ✅
- Check test coverage and add tests - TODO 🎁
peelee
- 2026.01.11
- I have sent an email to Bruce Wen (wenijinew) the author. - Waiting 🕰️
fastapi-cachex
- 2026.01.09
- PR: Add Dependabot configuration for version updates - Merged ✅
vcsp-guard
- 2025.12.27
- PR: add link to github - Merged ✅
- PR: add dependabot - Closed but implemented 🤔
- Issue: Local development, how to run the tests locally - ✅
- Learn: semgrep
- Learn: cliff
- Learn: build
- Learn: bandit
- Learn: pip-audit
- Learn: stefanzweifel/git-auto-commit-action
- Learn: softprops/action-gh-release
- Learn: pypa/gh-action-pypi-publish
conventional-pre-commit
- 2025.11.20
- git/COMMIT_EDITMSG: error Subject should be capitalized but found chore: - TODO 🎁
Biopython
- 2025.10.24
- Add type annotations - TODO 🎁
- chore: add type annotation to Bio/File.py - TODO 🎁
MoreBeautifulPython
- 2022.12.01
- Article: Test and CI for MoreBeautifulPython
- PR: Add a simple test and set up GitHub action to run it one every push - Merged ✅
farmworld
- 2022.12.03
- Article: CI for farmworld, a Python package - a failed attempt
- I sent a PR, but I don’t know what happened to it as the project was removed from GitHub. ❓
- I still have my fork 🍴 (there is no stand-alone fork emoji)
wsblib - Web Server Base Library.
- 2022.12.03
- Article: GitHub Action CI for wsblib Python
- PR: Add GitHub Actions - Merged ✅
col-spanish - A collection of tools to work with text write in Spanish (Colombia)
- 2022.12.04
- Article: GitHub Actions for Colombian Spanish
- PR: Add GitHub Actions - Rejected ❌ without explanation.
pcr_optimizer - A Python package to aid researchers in optimizing pcr protocols (Polymerase chain reaction)
- 2022.12.06
- Article: GitHub Actions CI for the pcr_optimizer Python package
- PR: Add GitHub Actions - Merged ✅
sdk-py - Decentralized Instant Messaging (Python SDK)
- 2022.12.12
- Article: CI for sdk-py Python packages
- PR: Add GitHub Action - Waiting 🕰️
core_curate_app - Curation functionalities for the curator core project.
- 2022.12.13
- Article: CI for a Python project of the National Institute of Standards and Technology
- PR: Add GitHub Actions - Rejected ❌ without explanation.
vfxpaths - A system analysis framework related to VFX common file operations.
- 2022.12.15
- Article: Failing CI to help fixing filesystem issues in a Python package
- PR: Add GitHub Action - Merged ✅

Some python projects

(Not fully categorized yet)

Generic

requests
jupyter
flask
pandas
pytest
numpy
allensdk
box2d
cv2
deeplabcut
functools
glob
gseapy
h5py
itertools
joblib
keras
matplot
matplotlib
mayavi
openpyxl
PIL
pygame
pyppt
ray
redirect
scipy
seaborn
skimage
statsmodels
tifffile
voila

ML

scikit-fmm
sklearn
tensorflow

Generic visualization

plotly
bokeh

Specialized

pcr_optimizer
GalSim is open-source software for simulating images of astronomical objects
farmworld
logomaker
BCAWT Automated tool for codon usage bias analysis for molecular evolution
An-Open-Source-Computational-Tool-for-Measuring-Bacterial-Biofilm-Morphology-and-Growth-Kinetics
MaLiAmPi Maximum Likelihood Amplicon Pipeline: An amplicon (PCR / 16S) microbiome pipeline.

These 3 try to solve the same problem: